Biology subjects

Tamames, J.

Publications and source records attributed to Tamames, J..

12 recordsLinked to original sources

bioRxiv2025

Temperature and pH universally govern protein diversity in hydrothermal spring communities, but they do so differently

A general understanding of how extreme temperature and pH might universally shape the evolution of protein variants is lacking. Importantly, while pH is differentially regulated in microbial compartments, temperature is not. We hypothesise that these variables may partly explain the within-genome variability in protein rates of single-celled organisms, since genes encode proteins allocated to different compartments. To test this hypothesis, we examine the number of unique sequence contributors assigned to a KEGG across species as a coarse proxy for accumulated evolutionary divergence. Under a naive null expectation, orthologs of equal abundance should be represented by a similar number of variants. We examine sequence diversity in 17 metagenomes from El Tatio geothermal field (Chile), spanning temperatures of 45-62 {degrees}C, and pH values of 7.2-9.3. At equal abundance, warmer temperature is weakly associated to more ortholog variants, while alkaline pH is associated to fewer (in the ranges examined). The inclusion of these variables in the model robustly improved the prediction of the community-level within-KO unique sequence contributors from metagenomic abundance. KO variant diversity in the periplasm was only significantly affected by pH increases, providing partial support to the compartment hypothesis.

evolutionary biology↗

bioRxiv2024

Microbial nitrogen guilds in the oceans: from the bathypelagic to the ocean surface

Ecological guilds quantify the incidence and extent of resource transformation functions, irrespective of the species involved. Therefore, tackling the microbial nitrogen guilds is key to our understanding of the oceanic nitrogen cycle, but quantitative estimates of guild contribution across varying depths and under specific environmental conditions have yet to be accomplished. In this study, we examine the main picoplankton guilds participating in nitrogen cycling within the low and mid-latitude ocean ecosystems, from the surface down to 4000 m, using data obtained from 75 samples belonging to 11 stations in the Malaspina (MP) dataset. In particular, we used a quantitative approach to investigate the stability of nitrogen acquisition and nitrogen-redox guilds separately. Our results showed that nitrogen acquisition guilds are more stable and redundant than nitrogen-redox guilds across depths and site specific conditions. For example, differential conditions such as nitrogen depletion and oxygen availability affected the two groups of guilds in different ways. These findings have implications for the understanding of global nitrogen fluxes and the biospheres functional diversification.

microbiology↗

bioRxiv2024

Nitrogen cycling during an Arctic bloom: from chemolithotrophy to nitrogen assimilation

In the Arctic, phytoplankton blooms are recurring phenomena occurring during the spring-summer seasons and influenced by the strong polar seasonality. Besides, bloom dynamics is affected by nutrient availability, especially nitrogen, which is the main limiting nutrient in the Arctic. This study aimed to investigate the changes in an Arctic microbial community during a phytoplankton bloom with a special focus on the nitrogen cycle. Using metagenomic and metatranscriptomic samples from the Dease Strait (Canada) from March to July (2014), we reconstructed 176 metagenome-assembled genomes. Bacteria dominated the microbial community, although archaea reached up to 25% of genomic abundance in early spring, when Nitrososphaeria archaea actively expressed genes associated with ammonia oxidation to nitrite (amt, amoA, nirK). The resulting nitrite was presumably further oxidized to nitrate by a Nitrospinota bacterium that highly expressed a nitrite oxidoreductase gene (nxr). Since May, the constant increase in chlorophyll a indicated the occurrence of a phytoplankton bloom, promoting the successive proliferation of different groups of chemoorganotrophic bacteria (Bacteroidetes, Alphaproteobacteria and Gammaproteobacteria). These bacterial taxa showed different strategies to obtain nitrogen, whether it be from organic or inorganic sources, according to the expression patterns of genes encoding transporters for nitrogen compounds. In contrast, during summer, the chemolithotrophic organisms thriving during winter, reduced their relative abundance and the expression of their catabolic genes. Based on the functional analysis of our data, we see a transition from a community where nitrogen-based chemolitotrophy plays a relevant role, to a chemoorganotrophic community based on the carbohydrates released during the phytoplankton bloom, where different groups specialize in different nitrogen sources.

microbiology↗

bioRxiv2023

Specialized Bacteroidetes dominate the Arctic Ocean during marine spring blooms

A metagenomic time series from Arctic seawater was obtained from the Canadian region of Dease Strait, to analyse the changes in bacterioplankton caused by the phytoplankton bloom that recurrently occurs in summer. This dataset documents the growth of bacterial clades specialised in the metabolism of plysaccharides, such as Bacteroidetes, along with the phytoplackton. These specialised taxa quickly displaced the microbial clades that dominate nutrient-poor waters during early spring, such as Archaea, Alpha- and Gammaproteobacteria. At the functional level, phyla Bacteroidetes, Planctomycetes and Verrucomicrobia showed higher contents of polysaccharide-degradation functions. Glycoside hydrolases revealed that the Bacteroidetes community shifted towards species with higher polysaccharide-degrading capabilities, targeting algal polysaccharides in summer. Regarding transporters, Bacteroidetes dominated SusC-TonB transporters and had an exclusive family of glycoside-binding proteins (SusD). These proteins were used to identify polysaccharide-utilisation loci that clustered transporters and polysaccharide-active enzymes, showing a higher level of specialisation towards polysaccharide use. Put together, all these genomic features point to the genetic adaptations that promote the dominance of Bacteroidetes during phytoplankton blooms.

microbiology↗

bioRxiv2023

Quantifying microbial guilds

The ecological role of microorganisms is of utmost importance due to their multiple interactions with the environment. However, assessing the contribution of individual taxonomic groups has proven difficult despite the availability of high throughput data, hindering our understanding of such complex systems. Here, we propose a quantitative definition of guild that is readily applicable to metagenomic data. Our framework focuses on the functional character of protein sequences, as well as their diversifying nature. First, we discriminate functional sequences from the whole sequence space corresponding to a gene annotation to then quantify their contribution to the guild composition across environments. In addition, we identify and distinguish functional implementations, which are sequence spaces that have different ways of carrying out the function. We demonstrate the value of our approach with two case studies: the ammonia oxidation and polyamine uptake guilds from the Malaspina circumnavigation cruise, revealing novel ecological dynamics of the latter in marine ecosystems. Thus, the quantification of guilds helps to assess the functional role of different taxonomic groups with profound implications on the study of microbial communities.

ecology↗

bioRxiv2023

In-situ metagenomics: A platform for rapid sequencing and analysis of metagenomes in less than one day

We present here a complete system for metagenomic analysis that allows performing the sequencing and analysis of a medium-size metagenome in less than one day. This unprecedented development was possible due to the conjunction of state-of-the art experimental and computational advances: a portable laboratory suitable for DNA extraction and sequencing with nanopore technology; the powerful metagenomic analysis pipeline SqueezeMeta, capable to provide a complete analysis in a few hours and using scarce computational resources; and tools for the automatic inspection of the results via a graphical user interface, that can be coupled to a web server to allow remote visualization of data (SQMtools and SQMxplore). We have tested the feasibility of our approach in the sequencing of the microbiota associated to volcanic rocks in La Palma, Canary Islands. Also, we did a two-day sampling campaign of marine waters in which the results obtained the first day guided the experimental design of the second day. This system offers the possibility of prospecting any habitat in a quick way, obtaining both taxonomic and functional information about the target microbiome.

genomics↗

bioRxiv2022

Cross-biome microbial networks reveal functional redundancy and suggest genome reduction through functional complementarity

Microbial communities are complex and dynamic entities, and their structure arises from the interplay of a multitude of factors, including the interactions of microorganisms with each other and with the environment. Since each extant community has a unique eco-evolutionary history, it might appear that contingency rather than general rules govern their assembly. In spite of this, there is evidence that some general assembly principles exist, at least to a certain extent. In this work, we sought to identify those principles by performing a cross-study, cross-biome meta-analysis of microbial occurrence data in more than 5,000 samples from ten different environmental groups. We adopted a novel algorithm that allows the same taxa to aggregate with different partners in different habitats, capturing the complexity of interactions inherent to natural microbial communities. We tried to decouple function from phylogeny, the environment, and genome size, in order to provide an unbiased characterization of phylogenetic and functional redundancy in environmental microbial assemblages. We then examined the phylogenetic and functional composition of the resulting inferred communities, and searched for global patterns of assembly both at the community level and in individual metabolic pathways. Our analysis of the resulting microbial assemblages highlighted that environmental communities are more functionally redundant than expected by chance. This effect is greater for communities appearing in more than one environment, suggesting a link between functional redundancy and environmental adaptation. In spite of this, certain pathways are observed in fewer taxa than expected by chance, suggesting the presence of auxotrophy, and presumably cooperation among community members, which is supported by our analysis of amino acid biosynthesis pathways. Furthermore, this hypothetical cooperation may play a role in genome reduction, since we observed a negative relationship between the size of bacterial genomes and the number of taxa of the community they belong to. Overall, our results provide a global characterization of environmental microbial communities, and offer design principles for engineering robust bacterial communities.

microbiology↗

bioRxiv2022

Bacterioplankton taxa compete for iron along the early spring-summer transition in the Arctic Ocean

Microbial assemblages under sea ice of Dease Strait, Canadian Arctic, were sequenced for metagenomes and metatranscriptomes of the small size fraction (0.2 to 3 {micro}m). The community from early March was typical for this season, with Alpha- and Gammaproteobacteria as the dominant taxa, followed by Thaumarchaeota and Bacteroidetes. Towards summer, Bacteroidetes and particularly the genus Polaribacter, became increasingly dominant, followed by the Gammaproteobacteria. Analysis of genes responsible for microbial acquisition of iron showed an abundance of ABC transporters for divalent cations and ferrous iron. The most abundant transporters, however, were the outer membrane TonB dependent transporters of iron-siderophore complexes. The abundance of iron acquisition genes suggested this element was essential for the microbial assemblage. Interestingly, Gammaproteobacteria were responsible for most of the siderophore synthesis genes. On the contrary, Bacteroidetes did not synthesize siderophores but accounted for most of the transporters, suggesting a role as cheaters in the competition for siderophores as public goods. Likely, this cheating ability of the Bacteroidetes contributed to their dominance in summer.

ecology↗

bioRxiv2021

M&Ms: A software for building realistic Microbial Mock communities

MotivationAdvances in sequencing technologies have triggered the development of many bioinformatic tools aimed to analyze these data. As these tools need to be tested, it is important to simulate datasets that resemble realistic conditions. Although there is a large amount of software dedicated to produce reads from in silico microbial communities, often the simulated data diverge widely from real situations. ResultsHere, we introduce M&Ms, a user-friendly open-source bioinformatic tool to produce realistic amplicon datasets from reference sequences, based on pragmatic ecological parameters. This tool creates sequence libraries for in silico microbial communities with user-controlled richness, evenness, microdiversity, and source environment. M&Ms allows the user to generate simple to complex read datasets based on real parameters that can be used in developing bioinformatic software or in benchmarking current tools. M&Ms also provides additional figures and files with extensive details on how each synthetic community is composed, so that users can make informed choices when designing their benchmarking pipelines. AvailabilityThe source code of M&Ms is freely available from https://github.com/ggnatalia/MMs Contactngarcia@cnb.csic.es

bioinformatics↗

bioRxiv2020

SQMtools: automated processing and visual analysis of 'omics data with R and anvi'o

BackgroundThe dramatic decrease in sequencing costs over the last decade has boosted the adoption of high-throughput sequencing applications as a standard tool for the analysis of environmental microbial communities. Nowadays even small research groups can easily obtain raw sequencing data. After that, however, non-specialists are faced with the double challenge of choosing among an ever-increasing array of analysis methodologies, and navigating the vast amounts of results returned by these approaches. ResultsHere we present a workflow that relies on the SqueezeMeta software for the automated processing of raw reads into annotated contigs and reconstructed genomes (bins). A set of custom scripts seamlessly integrates the output into the anvio analysis platform, allowing filtering and visual exploration of the results. Furthermore, we provide a software package with utility functions to expose the SqueezeMeta results to the R analysis environment. ConclusionsAltogether, our workflow allows non-expert users to go from raw sequencing reads to custom plots with only a few powerful, flexible and well-documented commands.

bioinformatics↗

bioRxiv2019

Assessing the performance of different approaches for functional and taxonomic annotation of metagenomes

Metagenomes can be analysed using different approaches and tools. One of the most important distinctions is the way to perform taxonomic and functional assignment, choosing between the usage of assemblies or the direct analysis of raw sequence reads instead. Many instances of each approach can be found in the literature, but to the best of our knowledge no evaluation of their different performances has been carried on, and we question if their results are comparable. We have studied this point by analysing several real and mock metagenomes using different methodologies and tools, and comparing the resulting taxonomic and functional profiles. Our results show that database completeness is the main factor determining the performance of the methods relying on direct read assignment either by homology, k-mer composition or similarity to marker genes, while methods relying on assembly and assignment of predicted genes are most influenced by sequencing depth, that in turn determines the completeness of the assembly. Although differences exist, taxonomic profiles are rather similar between raw read assignment and assembly assignment methods, while they are more divergent for methods based on k-mers and marker genes. Regarding functional annotation, analysis of raw reads retrieves more functions, but it also makes a significant number of over-predictions. Assembly methods are more advantageous as the size of the metagenome grows bigger.

bioinformatics↗

bioRxiv2018

SqueezeM, a fully automatic metagenomic analysis pipeline from reads to bins

The improvement of sequencing technologies has allowed the generalization of metagenomic sequencing, which has become a standard procedure for analysing the structure and functionality of microbiomes. The bioinformatic analysis of the sequencing results poses a challenge because it involves many different complex steps. SqueezeMeta is a full automatic pipeline for metagenomics/metatranscriptomics, covering all steps of the analysis. SqueezeMeta includes multi-metagenome support allowing the co-assembly of related metagenomes and the retrieval of individual genomes via binning procedures. SqueezeMeta features several unique characteristics: Co-assembly procedure or co-assembly of unlimited number of metagenomes via merging of individual assembled metagenomes, both with read mapping for estimation of the abundances of genes in each metagenome. It also includes binning and bin checking for retrieving individual genomes. Internal checks for the assembly and binning steps inform about the consistency of contigs and bins. Also, the results are stored in a mySQL database, where they can be easily exported and shared, and can be inspected anywhere using a flexible web interface allowing the easy creation of complex queries.\n\nWe illustrate the potential of SqueezeMeta by analyzing 32 gut metagenomes in a fully automatic way, allowing to retrieve several millions of genes and several hundreds of genomic bins.\n\nOne of the motivations in the development of SqueezeMeta was producing a software capable to run in small desktop computers, thus being amenable to all users and all settings. We were also able to co-assemble two of these metagenomes and complete the full analysis in less than one day using a simple laptop computer, illustrating the capacity of SqueezeMeta to run without high-performance computing infrastructure. SqueezeMeta is a complete system covering all steps in the analysis of metagenomes and metatranscriptomes, capable to work even in scarcity of computational resources. It is therefore adequate for in-situ, real time analysis of metagenomes produced by nanopore sequencing.\n\nSqueezeMeta can be downloaded from https://github.com/jtamames/SqueezeMeta

bioinformatics↗